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Open data
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Basic information
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Title | Plastid-encoded RNA polymerase | |||||||||||||||
![]() | Plastid-encoded RNA polymerase - composite map | |||||||||||||||
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![]() | Transcription / chloroplast / RNA polymerase / photosynthesis / GENE REGULATION | |||||||||||||||
Function / homology | ![]() DNA-directed RNA polymerase complex / chloroplast / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||||||||
![]() | Webster MW / Pramanick I / Vergara-Cruces A | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the plant plastid-encoded RNA polymerase. Authors: Ángel Vergara-Cruces / Ishika Pramanick / David Pearce / Vinod K Vogirala / Matthew J Byrne / Jason K K Low / Michael W Webster / ![]() ![]() Abstract: Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded ...Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded subunits similar to bacterial RNA polymerases (RNAPs) stably bound to a set of nuclear-encoded PEP-associated proteins (PAPs). PAPs are essential to PEP activity and chloroplast biogenesis, but their roles are poorly defined. Here, we present cryoelectron microscopy (cryo-EM) structures of native 21-subunit PEP and a PEP transcription elongation complex from white mustard (Sinapis alba). We identify that PAPs encase the core polymerase, forming extensive interactions that likely promote complex assembly and stability. During elongation, PAPs interact with DNA downstream of the transcription bubble and with the nascent mRNA. The models reveal details of the superoxide dismutase, lysine methyltransferase, thioredoxin, and amino acid ligase enzymes that are subunits of PEP. Collectively, these data provide a foundation for the mechanistic understanding of chloroplast transcription and its role in plant growth and adaptation. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 728.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 36.4 KB 36.4 KB | Display Display | ![]() |
Images | ![]() | 90.8 KB | ||
Filedesc metadata | ![]() | 12.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 620.1 KB | Display | ![]() |
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Full document | ![]() | 619.7 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8r5oMC ![]() 8r6sMC ![]() 8rasC ![]() 8rdjC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Plastid-encoded RNA polymerase - composite map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.5 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Plastid-encoded RNA polymerase
+Supramolecule #1: Plastid-encoded RNA polymerase
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit beta'
+Macromolecule #4: DNA-directed RNA polymerase subunit beta''
+Macromolecule #5: PAP1
+Macromolecule #6: PAP2
+Macromolecule #7: PAP3
+Macromolecule #8: PAP4
+Macromolecule #9: PAP5
+Macromolecule #10: PAP6
+Macromolecule #11: PAP7
+Macromolecule #12: PAP8
+Macromolecule #13: PAP9
+Macromolecule #14: PAP10
+Macromolecule #15: PAP11
+Macromolecule #16: PAP12
+Macromolecule #17: FLN2
+Macromolecule #18: PTAC18
+Macromolecule #19: ZINC ION
+Macromolecule #20: FE (III) ION
+Macromolecule #21: S-ADENOSYL-L-HOMOCYSTEINE
+Macromolecule #22: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 613537 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |